An interesting and somewhat under-documented is the configuration parameter disable_uw_upload. This entry in your configuration files will disable the SugarCRM system administrators’ ability to perform upgrades via the Upgrade Wizard, forcing the use of the silent upgrade tool.
SugarCRM’s OnDemand service uses this, presumably to ensure that they’re the ones handling all upgrades on the system (rightfully so), but if you were to get a backup of your OnDemand system, you will notice the configuration is unchanged. To manually upgrade your copy, you’ll need to modify config.php and set the disable_uw_upload parameter to false.
It’s worth noting, too, that this parameter is available and can be honored with your self-hosted SugarCRM instance (even CE). So if you want to securely lock-down your system and ensure none of your fellow sys-admin’s can run the upgrades, this is an excellent way of doing so.